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- PDB-8oyg: Crystal structure of ASBTNM in complex with pantoate -

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Basic information

Entry
Database: PDB / ID: 8oyg
TitleCrystal structure of ASBTNM in complex with pantoate
ComponentsTransporter
KeywordsTRANSPORT PROTEIN / Secondary Membrane Transporter
Function / homologyBile acid:sodium symporter/arsenical resistance protein Acr3 / Bile acid:sodium symporter / Sodium Bile acid symporter family / Sodium/solute symporter superfamily / membrane / : / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PANTOATE / Transporter
Function and homology information
Biological speciesNeisseria meningitidis MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBecker, P. / Cameron, A.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM118772 United States
CitationJournal: Biorxiv / Year: 2023
Title: Mechanism of substrate binding and transport in BASS transporters.
Authors: Becker, P. / Naughton, F.B. / Brotherton, D.H. / Pacheco-Gomez, R. / Beckstein, O. / Cameron, A.D.
History
DepositionMay 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6117
Polymers33,8371
Non-polymers7746
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-6 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.963, 89.364, 53.052
Angle α, β, γ (deg.)90.000, 124.400, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transporter


Mass: 33836.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Gene: NMB0705 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K0A9

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Non-polymers , 5 types, 31 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PAF / PANTOATE / 2,4-DIHYDROXY-3,3-DIMETHYL-BUTYRATE


Mass: 147.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.005 M Cadmium chloride hemi-(pentahydrate), 0.1 M Tris (pH 7.5), and 14% v/v PEG 500 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.3→44 Å / Num. obs: 14273 / % possible obs: 97.74 % / Redundancy: 3.9 % / Biso Wilson estimate: 35.55 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.1181 / Rpim(I) all: 0.06752 / Rrim(I) all: 0.1368 / Net I/σ(I): 5.74
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.4632 / Num. unique obs: 1201 / CC1/2: 0.804 / CC star: 0.944 / Rpim(I) all: 0.3397 / Rrim(I) all: 0.5779 / % possible all: 82.77

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→44 Å / SU ML: 0.265 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.5519
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2656 774 5.41 %
Rwork0.2261 25405 -
obs0.2282 14259 93.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.19 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2276 0 23 25 2324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00192347
X-RAY DIFFRACTIONf_angle_d0.44013200
X-RAY DIFFRACTIONf_chiral_restr0.0349398
X-RAY DIFFRACTIONf_plane_restr0.0029381
X-RAY DIFFRACTIONf_dihedral_angle_d11.2499799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.4591910.33911953X-RAY DIFFRACTION71.37
2.38-2.480.26351370.29732313X-RAY DIFFRACTION85.37
2.48-2.590.35221480.26972530X-RAY DIFFRACTION94.13
2.59-2.730.27351500.25362621X-RAY DIFFRACTION97.47
2.73-2.90.30651610.24122684X-RAY DIFFRACTION98.31
2.9-3.120.26341820.23772639X-RAY DIFFRACTION98.67
3.12-3.440.29681660.22322637X-RAY DIFFRACTION98.11
3.44-3.930.27841470.22032657X-RAY DIFFRACTION98.39
3.93-4.950.23491410.20432697X-RAY DIFFRACTION98.58
4.96-440.20951300.19672674X-RAY DIFFRACTION97.97
Refinement TLS params.Method: refined / Origin x: 9.03662140082 Å / Origin y: 11.2184429355 Å / Origin z: 16.5014518344 Å
111213212223313233
T0.357439728486 Å2-0.0168675035676 Å2-0.01453668863 Å2-0.371143781488 Å20.0027761041441 Å2--0.335360643441 Å2
L2.60225272828 °2-0.572443919535 °2-0.0400505566768 °2-2.58831059128 °20.314249997543 °2--1.43572263838 °2
S0.00342290116437 Å °0.0818292114561 Å °-0.0172096903075 Å °0.110332061135 Å °-0.04979166103 Å °-0.0557804108302 Å °-0.114829235686 Å °0.0891886256639 Å °8.16420023458E-6 Å °
Refinement TLS groupSelection details: all

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